Class FisherStrandFilter

  • All Implemented Interfaces:
    VariantFilter

    public class FisherStrandFilter
    extends Object
    implements VariantFilter
    Filters records based on the phred scaled p-value from the Fisher Strand test stored in the FS attribute.
    • Constructor Detail

      • FisherStrandFilter

        public FisherStrandFilter​(double maxPhredScalePValue)
    • Method Detail

      • headerLines

        public List<htsjdk.variant.vcf.VCFFilterHeaderLine> headerLines()
        Description copied from interface: VariantFilter
        Return VCF header lines that define filters that may be applied by the VariantFilter.
        Specified by:
        headerLines in interface VariantFilter
      • filter

        public String filter​(htsjdk.variant.variantcontext.VariantContext ctx)
        Description copied from interface: VariantFilter
        Check to see if the VariantContext should have a filter applied to it. If so return the filter string, otherwise return null.
        Specified by:
        filter in interface VariantFilter